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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagcatcacttttctatttaaaatgagttcaaccatatgttaaatttaagaggaagtttgtgctgcagaatgtgatcttttgtttggttgactgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTTGAAGCTATGTCTGCGATGAGAGAATCGTTTGCAACACTTCAAAATCTAA

Basic information

species Vitis vinifera
transcript Vv12s0059g01290.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 6
gagcatcacttttctatttaaaatgagtt--caaccatatg-ttaaatttaagaggaagtttg-tgctgcagaatgtgatcttttgtttggttgactgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTTGAAGCTATGTCTGCGATGAGAGAATCGTTTGCAACACTTCAAAATCTAA
     |  |   |  |   ||| ||      || |  ||||   |    |    |   ||||| | ||      |   ||  ||  |||   |   |  | ||||||||||| || || |||||||| ||||| ||||| |||||||| ||||||||||| |||||||| |  ||||| || |||||| |||||||||| || |
----gtttccaatgcaaacaaagtggagaggcatctgtatgaccatccctttttgtgtgtttgctactttcattttaaatgattattttttattttttcttcagGAAATGCTTCGGCCCATTCCTGTAGCTTTGGCATCTTGCACTCGGTTCTTTGAAGCCATGTCTGCCACAAGAGAGTCATTTGCATCACTTCAAAAACTGA

upper sequence: Vv12s0059g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G38820.1 (Glycine max), 3'ss of exon 5
----gagcatcacttttctatttaaa-atgagttcaaccatatgttaaatttaagaggaagtttgtgctgcagaatgtgatcttttgtttggttgactgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTTGAAGCTATGTCTGCGATGAGAGAATCGTTTGCAACACTTCAAAATCTAA
     |     |      |    |   ||| ||   |||||   ||   | |    |  | |||    |  | |   |||  || |  ||  |||  |  | ||||||||||| || || |||||||| ||||| ||||| |||||||| ||||||||||| |||||||| |  ||||| || |||||| |||||||||| || |
ttcccaatgcaaacaaagtgcacaggcatgtgtatgaccatcccttttttgtgtttgctacttt-cattttaaa---tgaaattattctttattgtttctt-cagGAAATGCTTCGGCCCATTCCTGTAGCTTTGGCATCTTGCACTCGGTTCTTTGAAGCCATGTCTGCCACAAGAGAGTCATTTGCATCACTTCAAAAACTGA

upper sequence: Vv12s0059g01290.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 5
gagcatcacttttctatttaaaatgagttcaaccatatgttaaatttaag---aggaagtttgtgctgcagaatgtgatcttttgtttggttgactga--tacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTTGAAGCTATGTCTGCGATGAGAGAATCGTTTGCAACACTTCAAAATCTAA
       ||||||  |  |||  ||      | ||  |||| | ||       |     | |   ||  |       |   ||| |||     ||  |  || |||||||||| || ||||| ||||| ||  |||| ||||||||  |||||||||| || |||||||||||||||||||| || || || |||||| | ||  
---tgctactttt--acgtaatgtgttgcataacagttgttgatttcggttttacatgctataatctcaatctctctactctttttttccccaacaaaattatagGAAATGCTGCGTCCAATACCTGTGGCACTAGCGTCATGCACGAGATTCTTTGAGGCCATGTCTGCGATGAGAGAATCATTCGCGACTCTTCAAGAGCTTC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|349826040|gb|FQ415845.1|FQ415845
EST:     CAGATTTCCAATGGACTCAAAATTTCCAGGAGCCACCTTCAGTATGGGGG                         GAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
genomic: CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGGgtatgtttat ... actgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
EST: gi|110365436|gb|EC928421.1|EC928421
EST:     CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGG                         GAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
genomic: CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGGgtatgtttat ... actgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
EST: gi|110386241|gb|EC950822.1|EC950822
EST:     CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGG                         GAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
genomic: CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGGgtatgtttat ... actgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
EST: gi|351019910|gb|FQ439727.1|FQ439727
EST:     CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGG                         GAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
genomic: CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGGgtatgtttat ... actgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
EST: gi|161721680|gb|FC069810.1|FC069810
EST:     CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGG                         GAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
genomic: CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGGgtatgtttat ... actgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
EST: gi|110401450|gb|EC968060.1|EC968060
EST:     CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGG                         GAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
genomic: CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGGgtatgtttat ... actgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
EST: gi|110413892|gb|EC979707.1|EC979707
EST:     CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGG                         GAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
genomic: CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGGgtatgtttat ... actgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
EST: gi|110374601|gb|EC939475.1|EC939475
EST:     CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGG                         GAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
genomic: CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGGgtatgtttat ... actgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
EST: gi|110382053|gb|EC938357.1|EC938357
EST:     CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGG                         GAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
genomic: CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGGgtatgtttat ... actgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
EST: gi|110374049|gb|EC938544.1|EC938544
EST:     CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGG                         GAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT
genomic: CAGATTTCCAATGGACTCAAAATTTCAAGGAGCCACCTTCAGTATGGGGGgtatgtttat ... actgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagaggaagtttgtgctgcagaatgtgatcttttgtttggttgactgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTTGAAGCTATGTCTGCGATGAGAGAATCGTTTGCAACACTTCAAAATCTAA
                                            gactgat  putative branch site (score: 3)
                                ttttgttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagcatcacttttctatttaaaatgagttcaaccatatgttaaatttaagaggaagtttgtgctgcagaatgtgatcttttgtttggttgactgatacagGAAATGCTCCGCCCAATTCCTGTTGCTTTAGCATCATGCACTCGATTCTTTGAAGCTATGTCTGCGATGAGAGAATCGTTTGCAACACTTCAAAATCTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- -catcact
- - - - - - - - - -aaaatga
- - - - - - - - - - - - - - tcaacca
- - - - - - - - - - - - - - - - - - - - - - - -aagagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgtg